Cleanup time symbols (#2096)

We have too many definitions of time ...

Author: dweindl

python/sdist/amici/de_export.py

@@ -51,6 +51,7 @@
 from .cxxcodeprinter import AmiciCxxCodePrinter, get_switch_statement
 from .de_model import *
 from .import_utils import (
+    amici_time_symbol,
     ObservableTransformation,
     SBMLException,
     generate_flux_symbol,
@@ -1012,7 +1013,7 @@ def transform_dxdt_to_concentration(species_id, dxdt):
                 # we need to flatten out assignments in the compartment in
                 # order to ensure that we catch all species dependencies
                 v = smart_subs_dict(v, si.symbols[SymbolId.EXPRESSION], "value")
-                dv_dt = v.diff(si.amici_time_symbol)
+                dv_dt = v.diff(amici_time_symbol)
                 # we may end up with a time derivative of the compartment
                 # volume due to parameter rate rules
                 comp_rate_vars = [
@@ -1733,7 +1734,7 @@ def _compute_equation(self, name: str) -> None:
             .replace("sigmarz", "sigmaz")
             .replace("dJrzdz", "dJrzdrz")
         )
-        time_symbol = sp.Matrix([symbol_with_assumptions("t")])
+        time_symbol = sp.Matrix([amici_time_symbol])
 
         if name in self._equation_prototype:
             self._equation_from_components(name, self._equation_prototype[name]())

python/sdist/amici/import_utils.py

@@ -54,10 +54,6 @@ def __init__(self, data):
 
 setattr(sys.modules["toposort"], "CircularDependencyError", CircularDependencyError)
 
-
-sbml_time_symbol = sp.Symbol("time", real=True)
-amici_time_symbol = sp.Symbol("t", real=True)
-
 annotation_namespace = "https://github.com/AMICI-dev/AMICI"
 
 
@@ -712,3 +708,7 @@ def strip_pysb(symbol: sp.Basic) -> sp.Basic:
     else:
         # in this case we will use sympy specific transform anyways
         return symbol
+
+
+sbml_time_symbol = symbol_with_assumptions("time")
+amici_time_symbol = symbol_with_assumptions("t")

python/sdist/amici/sbml_import.py

@@ -1253,10 +1253,6 @@ def _process_time(self) -> None:
         """
         Convert time_symbol into cpp variable.
         """
-        sbml_time_symbol = symbol_with_assumptions("time")
-        amici_time_symbol = symbol_with_assumptions("t")
-        self.amici_time_symbol = amici_time_symbol
-
         self._replace_in_all_expressions(sbml_time_symbol, amici_time_symbol)
 
     def _convert_event_assignment_parameter_targets_to_species(self):